BlockImpl (biojava 5.0.0 API)

java.lang.Object
- org.biojava.nbio.structure.align.multiple.AbstractScoresCache
- - org.biojava.nbio.structure.align.multiple.BlockImpl

All Implemented Interfaces:

Serializable, Cloneable, Block, ScoresCache
```
public class BlockImpl
extends AbstractScoresCache
implements Serializable, Block, Cloneable
```
General implementation of a Block that supports any type of sequential alignment with gaps.

Since:

4.1.0

Author:

Aleix Lafita

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

BlockImpl(BlockImpl b)
Copy constructor.

BlockImpl(BlockSet blockSet)
Constructor.

Constructors
Constructor and Description
`BlockImpl(BlockImpl b)` Copy constructor.
`BlockImpl(BlockSet blockSet)` Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clear()` Clear the cached scores.
`Block`	`clone()` Creates and returns an identical copy of this block.
`List<List<Integer>>`	`getAlignRes()` Returns the double List containing the aligned residues for each structure.
`List<Integer>`	`getAlignResCounts()` Returns the number of non null positions (residues) of each structure in the alignment Block.
`BlockSet`	`getBlockSet()` Returns the parent BlockSet of the Block.
`int`	`getCoreLength()` Returns the number of aligned positions (columns) without gaps in the Block.
`int`	`getFinalIndex(int str)` Calculates and returns the last position of the specified structure in the alignment that is not null.
`int`	`getFinalResidue(int str)` Calculates and returns the last residue of the specified structure in the alignment that is not null.
`int`	`getStartIndex(int str)` Calculates and returns the first position of the specified structure in the alignment that is not null.
`int`	`getStartResidue(int str)` Calculates and returns the first residue of the specified structure in the alignment that is not null.
`int`	`length()` Returns the total number of aligned positions (columns) in the Block.
`void`	`setAlignRes(List<List<Integer>> alignRes)` Set the double List containing the aligned residues for each structure.
`void`	`setBlockSet(BlockSet parent)` Set the back-reference to its parent BlockSet.
`int`	`size()` Returns the number of aligned structures (rows) in the Block.
`String`	`toString()`
`protected void`	`updateCoreLength()`

Methods inherited from class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
clone, getScore, getScores, putScore

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.nbio.structure.align.multiple.ScoresCache
getScore, getScores, putScore

- Constructor Detail
  - BlockImpl
```
public BlockImpl(BlockSet blockSet)
```
    Constructor. Links also the parent to this instance, by adding the Block to the parent's list.
    
    Parameters:
    
    blockSet - the parent BlockSet of the BlockImpl instance.
  - BlockImpl
```
public BlockImpl(BlockImpl b)
```
    Copy constructor.
    
    Parameters:
    
    b - BlockImpl object to be copied.
- Method Detail
  - clone
```
public Block clone()
```
    Description copied from interface: Block
    
    Creates and returns an identical copy of this block.
    
    Specified by:
    
    clone in interface Block
    
    Overrides:
    
    clone in class Object
    
    Returns:
    
    Block identical copy of this object.
  - clear
```
public void clear()
```
    Description copied from class: AbstractScoresCache
    
    Clear the cached scores. This frees memory after the alignment changed.
    
    Specified by:
    
    clear in interface Block
    
    Overrides:
    
    clear in class AbstractScoresCache
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - setBlockSet
```
public void setBlockSet(BlockSet parent)
```
    Description copied from interface: Block
    
    Set the back-reference to its parent BlockSet.
    
    Specified by:
    
    setBlockSet in interface Block
    
    Parameters:
    
    parent - the parent BlockSet.
    
    See Also:
    
    Block.getBlockSet()
  - getBlockSet
```
public BlockSet getBlockSet()
```
    Description copied from interface: Block
    
    Returns the parent BlockSet of the Block. Returns null if there is no referenced object.
    
    Specified by:
    
    getBlockSet in interface Block
    
    Returns:
    
    BlockSet the parent BlockSet of the Block, or null.
    
    See Also:
    
    Block.setBlockSet(BlockSet)
  - getAlignRes
```
public List<List<Integer>> getAlignRes()
```
    Description copied from interface: Block
    
    Returns the double List containing the aligned residues for each structure.
    alignRes.get(structure).get(residue) = alignRes.get(size).get(length).
    
    Specified by:
    
    getAlignRes in interface Block
    
    Returns:
    
    List a double List of aligned residues for each structure.
    
    See Also:
    
    #setAlignRes()
  - setAlignRes
```
public void setAlignRes(List<List<Integer>> alignRes)
```
    Description copied from interface: Block
    
    Set the double List containing the aligned residues for each structure.
    
    Specified by:
    
    setAlignRes in interface Block
    
    Parameters:
    
    alignRes - a double List of Integers with the aligned residues.
    
    See Also:
    
    Block.getAlignRes()
  - length
```
public int length()
```
    Description copied from interface: Block
    
    Returns the total number of aligned positions (columns) in the Block.
    
    Specified by:
    
    length in interface Block
    
    Returns:
    
    int number of aligned residues.
    
    See Also:
    
    Block.getCoreLength();, Block.size()
  - size
```
public int size()
```
    Description copied from interface: Block
    
    Returns the number of aligned structures (rows) in the Block.
    
    Specified by:
    
    size in interface Block
    
    Returns:
    
    int number of aligned structures.
    
    See Also:
    
    Block.length(), Block.getCoreLength()
  - getCoreLength
```
public int getCoreLength()
```
    Description copied from interface: Block
    
    Returns the number of aligned positions (columns) without gaps in the Block.
    
    Specified by:
    
    getCoreLength in interface Block
    
    Returns:
    
    int number of aligned residues.
    
    See Also:
    
    #updateCoreLength(), Block.length(), Block.size()
  - updateCoreLength
```
protected void updateCoreLength()
```
  - getStartIndex
```
public int getStartIndex(int str)
```
    Description copied from interface: Block
    
    Calculates and returns the first position of the specified structure in the alignment that is not null. This will return the aligment index, not the reisude aligned in that position.
    
    Specified by:
    
    getStartIndex in interface Block
    
    Parameters:
    
    str - structure index
    
    Returns:
    
    the first non null aligned position of the structure
  - getStartResidue
```
public int getStartResidue(int str)
```
    Description copied from interface: Block
    
    Calculates and returns the first residue of the specified structure in the alignment that is not null. This will return the aligned residue, not the alignment index.
    
    Specified by:
    
    getStartResidue in interface Block
    
    Parameters:
    
    str - structure index
    
    Returns:
    
    the first non null aligned residue of the structure
  - getFinalIndex
```
public int getFinalIndex(int str)
```
    Description copied from interface: Block
    
    Calculates and returns the last position of the specified structure in the alignment that is not null. This will return the aligment index, not the reisude aligned in that position.
    
    Specified by:
    
    getFinalIndex in interface Block
    
    Parameters:
    
    str - structure index
    
    Returns:
    
    the last non null aligned position of the structure
  - getFinalResidue
```
public int getFinalResidue(int str)
```
    Description copied from interface: Block
    
    Calculates and returns the last residue of the specified structure in the alignment that is not null. This will return the aligned residue, not the alignment index.
    
    Specified by:
    
    getFinalResidue in interface Block
    
    Parameters:
    
    str - structure index
    
    Returns:
    
    the last non null aligned residue of the structure
  - getAlignResCounts
```
public List<Integer> getAlignResCounts()
```
    Description copied from interface: Block
    
    Returns the number of non null positions (residues) of each structure in the alignment Block. The values can be used to compute the coverages.
    
    Specified by:
    
    getAlignResCounts in interface Block
    
    Returns:
    
    List of residue counts for each structure

Class BlockImpl

Constructor Summary

Method Summary

Methods inherited from class org.biojava.nbio.structure.align.multiple.AbstractScoresCache

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.nbio.structure.align.multiple.ScoresCache

Constructor Detail

BlockImpl

BlockImpl

Method Detail

clone

clear

toString

setBlockSet

getBlockSet

getAlignRes

setAlignRes

length

size

getCoreLength

updateCoreLength

getStartIndex

getStartResidue

getFinalIndex

getFinalResidue

getAlignResCounts